Missigness before removing buffer
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missingness plots, missing values: 14853 out of 113400 (13.10%)
Missingness after removing buffer
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missingness plots, missing values: 10227 out of 90720 (11.27%)
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features filtered, 50.00%, 39 of 630 removed
Missingness after filtering metabolites with more than 50% missing values per group
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missingness plots, missing values: 6331 out of 85104 (7.44%)
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sample boxplot, aes: color=Buffer
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sample boxplot, aes: color=tissue
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quotient normalization based on 36 reference samples and 511 variables: ~
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quotient normalization based on 36 reference samples and 511 variables: Buffer == “80% Meth + 20% H2O”
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dilution factor plot, ‘Buffer’
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sample boxplot, aes: color=Buffer
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log2.000000
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sample boxplot, aes: color=Buffer
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flagged 0 univariate outliers
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Dataset info: 144 samples, 591 features; 25 sample annotation fields, 10 feature annotation fields
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Data exported to Excel file ‘PreprocessedData.xlsx’
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UMAP, label_col: , aes: color=Buffer, size=2.5
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Heatmap of assay data.
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UMAP, label_col: , aes: color=tissue, size=2.5
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Heatmap of assay data.
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PCA, scores, label_col: , aes: color=Buffer, shape=tissue, size=2.5
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univariate lm, ~Buffer
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Multiple testing correction of ‘Buffer met’ using ‘BH’
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‘Buffer met’ info
Samples: 50% Meth + 50% H2O: 36, 50% Meth + 50% PBS: 36, 80% Meth + 20% H2O: 36, 80% Meth + 20% PBS: 36 /// features: p.adj < 0.05, 125 of 591
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Exported sheets ‘Buffer met’ to Excel file ‘BufferAnalysis.xlsx’
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P-value histograms for Buffer met
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Feature
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univariate lm, ~tissue
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Multiple testing correction of ‘Tissue met’ using ‘BH’
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‘Tissue met’ info
Samples: fat: 48, liver: 48, muscle: 48 /// features: p.adj < 0.05, 360 of 591
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Exported sheets ‘Buffer met, Tissue met’ to Excel file ‘TissueAnalysis.xlsx’
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P-value histograms for Tissue met
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bar plot for comparison Buffer met, Tissue met, by Class, filtered for p.adj < 0.05, using count
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bar plot for comparison Buffer met, Tissue met, by Class, filtered for p.adj < 0.05, using fraction
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Pheatmap of stat results. Colors represent (sign(statistic) * -log10(p.adj)))
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comparison plot between ‘Buffer met’ and ‘Tissue met’
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GeneNet partial correlation
WARNING: Large data frame (174345 rows). Displaying first 1000 rows.
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Multiple testing correction of ‘GGM’ using ‘BH’
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Correlation Network, aes: GGM